Using Allele-Specific PCR to Genotype Beefalo

Abstract

The near extermination of the American bison (Bison bison) in the late nineteenth century resulted from overhunting for pelts and sport. This reduced a population of tens of millions to only a few hundred individuals by the early twentieth century. As bison populations recovered, their favorable traits, like temperature resistance and reduced calving, made them attractive for crossbreeding with domestic cattle (Bos taurus). This led to the development of the hybrid known as beefalo. Today, beefalo are defined by federal standards as containing between 17% and 37.5% bison ancestry. However, this percentage is typically estimated through breeding records rather than direct genetic analysis, resulting in inconsistent expression of bison traits among animals reported as having similar ancestry. Consequently, farmers seek more precise genetic control over calf ancestry percentages and trait inheritance.

The central goal of this research is to develop a more accurate genetic method for tracking bison DNA inheritance in beefalo. Specifically, this study investigates whether single nucleotide polymorphisms between species (sSNPs) can be used to distinguish cattle and bison alleles from each other, improving predictions of bison trait inheritance. Current genetic testing methods rely on a limited number of markers and do not adequately represent all 30 chromosome pairs.

This study utilizes tail hair follicles and a Chelex-based extraction method to isolate DNA. Exonic sequences from Bison bison and Bos taurus genomes were compared using Geneious Prime to identify candidate sSNPs. Allele-specific PCR primers were designed for 60 loci distributed across all bovine chromosomes. Primer specificity and successful amplification were evaluated using PCR and gel electrophoresis. Results indicate that the mismatch primer design can effectively and successfully amplify a subset of targeted sSNPs to genetically distinguish sequences of Bison bison from Bos taurus, however amplification success varied among loci. Future work will expand sSNP coverage, verify primer specificity across diverse cattle breeds, and associate SNPs with desired traits.